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# ===========================================================================
# SeqAn - The Library for Sequence Analysis
# ===========================================================================
# File: /apps/yara/CMakeLists.txt
#
# CMakeLists.txt file for yara.
# ===========================================================================
cmake_minimum_required (VERSION 3.0.0)
project (seqan_apps_yara CXX)
message (STATUS "Configuring apps/yara")
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "mips")
message (STATUS " Not building yara on mips due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "mipsel")
message (STATUS " Not building yara on mipsel due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "armhf")
message (STATUS " Not building yara on armhf due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "sh4")
message (STATUS " Not building yara on sh4 due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "armel")
message (STATUS " Not building yara on armel due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "kfreebsd-i386")
message (STATUS " Not building yara on kfreebsd-i386 due to memory requirements.")
return ()
endif ()
if ("$ENV{DEB_BUILD_ARCH}" STREQUAL "hurd-i386")
message (STATUS " Not building yara on hurd-i386 due to memory requirements.")
return ()
endif ()
# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------
if (COMPILER_MSVC)
message (STATUS "Yara is currently not build on Microsoft Visual because it requires OpenMP 3.0.")
return ()
endif ()
# Search SeqAn and select dependencies.
if (NOT "${SEQAN_BUILD_SYSTEM}" STREQUAL "DEVELOP")
find_package (OpenMP)
find_package (ZLIB)
find_package (BZip2)
find_package (SeqAn CONFIG REQUIRED)
endif ()
# Warn if OpenMP was not found.
if (NOT OPENMP_FOUND)
message (STATUS " OpenMP 3.0 not found: building yara without multi-threading.")
endif (NOT OPENMP_FOUND)
# Warn if Zlib was not found.
if (NOT ZLIB_FOUND)
message (STATUS " Zlib not found: building yara without gzipped input and BAM output.")
endif (NOT ZLIB_FOUND)
# Warn if BZip2 was not found.
if (NOT BZIP2_FOUND)
message (STATUS " BZip2 not found: building yara without bzipped input.")
endif (NOT BZIP2_FOUND)
# ----------------------------------------------------------------------------
# App-Level Configuration
# ----------------------------------------------------------------------------
set (SEQAN_APP_VERSION "0.9.11")
option (YARA_LARGE_CONTIGS "Set to OFF to disable support for more than 32k contigs or contigs longer than 4Gbp." ON)
if (YARA_LARGE_CONTIGS AND NOT SEQAN_TRAVIS_BUILD)
add_definitions (-DYARA_LARGE_CONTIGS=1)
endif (YARA_LARGE_CONTIGS AND NOT SEQAN_TRAVIS_BUILD)
# ----------------------------------------------------------------------------
# Disable Compiler Warnings
# ----------------------------------------------------------------------------
# Disables warning about conversion from 64 bit to 32 bit integrals.
# Note that there is a runtime exception thrown if the type is not sufficient.
# Unfortunately the VC does not detect it.
if (MSVC)
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} /wd4244") # When compiling on 32 bit windows.
set (SEQAN_CXX_FLAGS "${SEQAN_CXX_FLAGS} /wd4267") # When compiling on 64 bit windows.
endif (MSVC)
# ----------------------------------------------------------------------------
# Build Setup
# ----------------------------------------------------------------------------
# Add include directories.
include_directories (${SEQAN_INCLUDE_DIRS})
# Add definitions set by find_package (SeqAn).
add_definitions (${SEQAN_DEFINITIONS})
# Add definitions set by the build system.
add_definitions (-DSEQAN_REVISION="${SEQAN_REVISION}")
add_definitions (-DSEQAN_DATE="${SEQAN_DATE}")
add_definitions (-DSEQAN_APP_VERSION="${SEQAN_APP_VERSION}")
# Add CXX flags found by find_package (SeqAn).
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SEQAN_CXX_FLAGS}")
# Update the list of file names below if you add source files to your application.
add_executable(yara_indexer indexer.cpp
misc_tags.h
misc_timer.h
misc_options.h
misc_types.h
store_seqs.h
bits_matches.h
index_fm.h)
add_executable(yara_mapper mapper.cpp
mapper.h
mapper_collector.h
mapper_classifier.h
mapper_ranker.h
mapper_filter.h
mapper_extender.h
mapper_verifier.h
mapper_aligner.h
mapper_writer.h
basic_alphabet.h
file_pair.h
file_prefetched.h
store_seqs.h
misc_tags.h
misc_timer.h
misc_options.h
misc_types.h
bits_reads.h
bits_hits.h
bits_matches.h
bits_context.h
bits_seeds.h
bits_bucket.h
find_extender.h
find_verifier.h
index_fm.h)
# Add dependencies found by find_package (SeqAn).
target_link_libraries (yara_indexer ${SEQAN_LIBRARIES})
target_link_libraries (yara_mapper ${SEQAN_LIBRARIES})
# ----------------------------------------------------------------------------
# Installation
# ----------------------------------------------------------------------------
# Set variables for installing, depending on the selected build type.
if (NOT SEQAN_PREFIX_SHARE_DOC)
seqan_setup_install_vars (yara)
endif (NOT SEQAN_PREFIX_SHARE_DOC)
# Install yara in ${PREFIX}/bin directory
install (TARGETS yara_indexer yara_mapper
DESTINATION ${CMAKE_INSTALL_BINDIR})
# Install non-binary files for the package to "." for app builds and
# ${PREFIX}/share/doc/yara for SeqAn release builds.
install (FILES LICENSE README.rst
DESTINATION ${SEQAN_PREFIX_SHARE_DOC})
# ----------------------------------------------------------------------------
# App Test
# ----------------------------------------------------------------------------
seqan_add_app_test (yara)
# ----------------------------------------------------------------------------
# Setup Common Tool Description for Generic Workflow Nodes
# ----------------------------------------------------------------------------
# Include executable yara_mapper in CTD structure.
set (SEQAN_CTD_EXECUTABLES ${SEQAN_CTD_EXECUTABLES}
yara_indexer yara_mapper CACHE INTERNAL "")
# ----------------------------------------------------------------------------
# CPack Install
# ----------------------------------------------------------------------------
if (SEQAN_BUILD_SYSTEM STREQUAL "APP:yara")
set (CPACK_PACKAGE_NAME "yara")
set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "Yara - Yet Another Read Aligner")
set (CPACK_DEBIAN_PACKAGE_MAINTAINER "Enrico Siragusa <enrico.siragusa@fu-berlin.de>")
set (CPACK_PACKAGE_VENDOR "SeqAn Team, FU Berlin")
set (CPACK_PACKAGE_DESCRIPTION_FILE "${CMAKE_CURRENT_SOURCE_DIR}/README.rst")
seqan_configure_cpack_app (yara "yara")
endif (SEQAN_BUILD_SYSTEM STREQUAL "APP:yara")
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